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BMRB: 30064

5J8T

NMR structure of Excalibur domain of CbpL

Authors

Pantoja-Uceda, D., Trevino, M.A., Bruix, M.

Assembly

Choline binding protein (E.C.3.2.1.96)

Entity

1. Choline binding protein (E.C.3.2.1.96), entity 1 (polymer), 47 monomers, 5138.403 Da Detail

GASEENIHFS SCKEAWANGY SDIHEGEPGY SAKLDRDHDG VACELKN

2. Choline binding protein (E.C.3.2.1.96), entity CA (non-polymer), 40.078 Da

Total weight

5178.481 Da

Max. entity weight

5138.403 Da

Source organism

Streptococcus pneumoniae

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.4 %, Completeness (bb): 97.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.4 % (470 of 503)	98.5 % (256 of 260)	85.5 % (165 of 193)	98.0 % (49 of 50)
Backbone	97.5 % (273 of 280)	98.0 % (96 of 98)	97.1 % (132 of 136)	97.8 % (45 of 46)
Sidechain	88.7 % (235 of 265)	98.8 % (160 of 162)	71.7 % (71 of 99)	100.0 % (4 of 4)
Aromatic	48.0 % (24 of 50)	92.0 % (23 of 25)	0.0 % (0 of 24)	100.0 % (1 of 1)
Methyl	100.0 % (30 of 30)	100.0 % (15 of 15)	100.0 % (15 of 15)

1. entity 1

GASEENIHFS SCKEAWANGY SDIHEGEPGY SAKLDRDHDG VACELKN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	Excalibur domain of CbpL	natural abundance		0.5 mM
5	CaCl2	natural abundance		3 mM
6	DSS	natural abundance		1 %

LACS Plot; CA

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.27 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5J8T, Strand ID: A Detail

Release date

2016-12-07

Citation

Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L (CbpL) Contributing to Pneumococcal Pathogenesis
Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gomez-Mejia, A., Pantoja-Uceda, D., Trevino, M.A., Voss, F., Abdullah, M.R., Galan-Bartual, S., Seinen, J., Sanchez-Murcia, P.A., Gago, F., Bruix, M., Hammerschmidt, S., Hermoso, J.A.
Sci. Rep. (2016), 6, 38094-38094, PubMed 27917891 , DOI 10.1038/srep38094 , Abstract

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	Excalibur domain of CbpL	natural abundance		0.5 mM
5	CaCl2	natural abundance		3 mM
6	DSS	natural abundance		1 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	Excalibur domain of CbpL	natural abundance		0.5 mM
5	CaCl2	natural abundance		3 mM
6	DSS	natural abundance		1 %

5 3D HNCO

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

6 3D HNCOi

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

7 3D HNCA

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

8 3D HNCAi

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

9 3D HNCACB

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

10 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

11 3D H(CCCO)NH

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

12 3D (H)CC(CO)NH

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

13 3D HC(C)H-TOCSY

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

14 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

15 3D H(NCOCA)NH

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

16 3D (H)N(COCA)NH

Instrument

Bruker Avance - 800 MHz equiped with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Excalibur domain of CbpL	[U-99% 13C; U-99% 15N]		0.5 mM
2	CaCl2	natural abundance		3 mM
3	DSS	natural abundance		1 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30064_5j8t.nef
Input source #2: Coordindates	5j8t.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:35:CYS:SG	A:66:CYS:SG	reduced, CA 55.452, CB 33.316 ppm	reduced, CA 53.021, CB 31.308 ppm	2.047

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:35:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:35:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:37:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:37:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:39:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:39:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:44:GLU:OE1	2:1:CA:CA	unknown	unknown	n/a
1:44:GLU:OE2	2:1:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CA	CALCIUM ION	Distance restraints

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-----30--------40--------50--------60--------70
GASEENIHFSSCKEAWANGYSDIHEGEPGYSAKLDRDHDGVACELKN
|||||||||||||||||||||||||||||||||||||||||||||||
GASEENIHFSSCKEAWANGYSDIHEGEPGYSAKLDRDHDGVACELKN
--------10--------20--------30--------40-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	47	0	0	100.0

Content subtype: combined_30064_5j8t.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	9		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	471		100.0 (chain: A, length: 47)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	723 (1)	noe	97.9 (chain: A, length: 47)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	11 (1)	undefined	12.8 (chain: A, length: 47), 100.0 (chain: B, length: 1)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	58 (58)	.	80.9 (chain: A, length: 47)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 257
  - ¹³C chemical shifts: 165
  - ¹⁵N chemical shifts: 49
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 97.9%
- Total number of restraints: 723
- Weight of restraints: 1.0 (723)
- Potential type of restraints: upper-bound-parabolic (723)
- Range of distance target values: 2.59, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 12.8%
    - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
  - Total number of restraints: 11
  - Weight of restraints: 1.0 (11)
  - Potential type of restraints: upper-bound-parabolic (11)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 80.9%
- Total number of restraints: 58
- Total number of restraints per polymer type: 58
- Weight of restraints: 1.0 (58)
- Potential type of restraints: square-well-parabolic (58)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Choline-binding Protein L, Excalibur, Pneumococcal Adhesion, hydrolase